Publications

See a list of publications below or visit the Photonics academic staff page and click on a particular  member of staff to access their personal web page, which includes a list of their own publications.

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  • Journal article
    McCall M, Koufidis S, 2022,

    Reverse circular Bragg phenomenon

    , Physical Review Research, Vol: 4, ISSN: 2643-1564

    he problem of axial propagation of circularly polarized light in a circularly birefringent structurally chiral medium is exactly solved via full electromagnetic analysis. Underlying symmetries of the system's characteristic matrix reveal interesting insights, which are confirmed by coupled wave theory. For extreme values of chirality, a reverse circular Bragg resonance arises in the negative refraction regime where handedness reversal of counterpart modes occurs. A condition is identified under which circular birefringence precisely offsets structural chirality, rendering the medium simply linearly birefringent. Manufacturing such a medium is feasible via current metamedia and inorganic materials technology and has applications in optics, optoelectronics, and sensing.
  • Journal article
    Hong W, Wright T, Sparks H, Dvinskikh L, MacLeod K, Paterson C, Dunsby Cet al., 2022,

    Adaptive light-sheet fluorescence microscopy with a deformable mirror for video-rate volumetric imaging

    , Applied Physics Letters, Vol: 121, Pages: 1-7, ISSN: 0003-6951

    Light-sheet fluorescence microscopy (LSFM) achieves optically sectioned imaging with the relatively low photobleaching and phototoxic effect. To achieve high-speed volumetric LSFM imaging without perturbing the sample, it is necessary to use some form of remote refocusing in the detection beam path. Previous work used electrically tunable lenses, tunable acoustic gradient index of refraction lenses, or the remote-refocusing approach of Botcherby et al. [Opt. Lett. 32(14), 2007 (2007)] to achieve remote refocusing. However, these approaches generally only provide low-order defocus correction, which is not compatible with higher-NA objectives that require higher order defocus corrections or reduce the optical throughput. In order to simultaneously achieve high-speed remote refocusing and correct system aberrations, we employ a deformable mirror in the detection path that is capable of providing higher orders of defocus and aberration correction in an optical system with an NA of 0.72–0.75. We demonstrate high-speed volumetric imaging at 26.3 volumes per second and 35 frames per volume for a defocus range of −50 to 50 μm.
  • Journal article
    Ribenek VA, Korobko DA, Fotiadi AA, Taylor JRet al., 2022,

    Supermode noise mitigation and repetition rate control in a harmonic mode-locked fiber laser implemented through the pulse train interaction with co-lased CW radiation: publisher's note

    , OPTICS LETTERS, Vol: 47, Pages: 5582-5582, ISSN: 0146-9592
  • Journal article
    Kinsler P, McCall MW, Oulton RF, Clark ASet al., 2022,

    The surprising persistence of time-dependent quantum entanglement

    , New Journal of Physics, Vol: 24, Pages: 1-14, ISSN: 1367-2630

    The mismatch between elegant theoretical models and the detailed experimental reality is particularly pronounced in quantum nonlinear interferometry (QNI). In stark contrast to theory, experiments contain pump beams that start in impure states and that are depleted, quantum noise that affects—and drives—any otherwise gradual build up of the signal and idler fields, and nonlinear materials that are far from ideal and have a complicated time-dependent dispersive response. Notably, we would normally expect group velocity mismatches to destroy any possibility of measurable or visible entanglement, even though it remains intact—the mismatches change the relative timings of induced signal–idler entanglements, thus generating 'which path' information. Using an approach based on the positive-P representation, which is ideally suited to such problems, we are able to keep detailed track of the time-domain entanglement crucial for QNI. This allows us to show that entanglement can be—and is—recoverable despite the obscuring effects of real-world complications; and that recovery is attributable to an implicit time-averaging present in the detection process.
  • Journal article
    Tang M, 2022,

    Super-resolution ultrasound localization microscopy of microvascular structure and flow for distinguishing metastatic lymph nodes – an initial human study

    , Ultraschall in der Medizin, Vol: 43, Pages: 592-598, ISSN: 0172-4614

    Purpose Detecting and distinguishing metastatic lymph nodes (LNs) from those with benign lymphadenopathy are crucial for cancer diagnosis and prognosis but remain a clinical challenge. A recent advance in super-resolution ultrasound (SRUS) through localizing individual microbubbles has broken the diffraction limit and tracking enabled in vivo noninvasive imaging of vascular morphology and flow dynamics at a microscopic level. In this study we hypothesize that SRUS enables quantitative markers to distinguish metastatic LNs from benign ones in patients with lymphadenopathy.Materials and Methods Clinical contrast-enhanced ultrasound image sequences of LNs from 6 patients with lymph node metastasis and 4 with benign lymphadenopathy were acquired and motion-corrected. These were then used to generate super-resolution microvascular images and super-resolved velocity maps. From these SRUS images, morphological and functional measures were obtained including micro-vessel density, fractal dimension, mean flow speed, and Local Flow Direction Irregularity (LFDI) measuring the variance in local flow direction. These measures were compared between pathologically proven reactive and metastasis LNs.Results Our initial results indicate that the difference in the indicator of flow irregularity (LFDI) derived from the SRUS images is statistically significant between the two groups. The LFDI is 60% higher in metastatic LNs compared with reactive nodes.Conclusion This pilot study demonstrates the feasibility of super-resolution ultrasound for clinical imaging of lymph nodes and the potential of using the irregularity of local blood flow directions afforded by SRUS for the characterization of LNs.
  • Journal article
    Ribenek VA, Korobko DA, Fotiadi AA, Taylor JRet al., 2022,

    Supermode noise mitigation and repetition rate control in harmonic mode-locked fiber laser implemented through the pulse train interaction with co-lased CW radiation

    , OPTICS LETTERS, Vol: 47, Pages: 5236-5239, ISSN: 0146-9592
  • Journal article
    Hong Y, Taengnoi N, Bottrill KRH, Thipparapu NK, Wang Y, Sahu JK, Richardson DJ, Petropoulos Pet al., 2022,

    Experimental demonstration of single-span 100-km O-band 4x50-Gb/s CWDM direct-detection transmission

    , OPTICS EXPRESS, Vol: 30, Pages: 32189-32203, ISSN: 1094-4087
  • Journal article
    Calvarese M, Paie P, Candeo A, Calisesi G, Ceccarelli F, Valentini G, Osellame R, Gong H, Neil M, Bragheri F, Bassi Aet al., 2022,

    Integrated optical device for Structured Illumination Microscopy

    , OPTICS EXPRESS, Vol: 30, Pages: 30246-30259, ISSN: 1094-4087
  • Journal article
    Coney AT, Beecher S, Damzen MJ, Elder Iet al., 2022,

    High-energy Q-switched Nd:YAG oscillator and amplifier development for large-mode, low-alignment sensitivity applications

    , LASER PHYSICS LETTERS, Vol: 19, ISSN: 1612-2011
  • Journal article
    Lightley J, Kumar S, Garcia E, Alexandrov Y, Dunsby C, Neil MAA, French PMWet al., 2022,

    Robust, single-shot, optical autofocus system utilizing cylindrical lenses to provide high precision and long range of operation

    <jats:title>ABSTRACT</jats:title><jats:p>We present a robust, “real-time” optical autofocus system for microscopy that provides high accuracy (&lt;230 nm) and long range (∼130 µm) with a 1.4 numerical aperture oil immersion objective lens. This autofocus can operate in a closed loop, single-shot functionality over a range of ±37.5 µm and can also operate as a 2-step process up to ±68 µm. A real-time autofocus capability is useful for experiments with long image data acquisition times, including single molecule localization microscopy, that may be impacted by defocusing resulting from drift of components, e.g., due to changes in temperature or mechanical drift. It is also vital for automated slide scanning or multiwell plate imaging where the sample may not be in the same horizontal plane for every field of view during the image data acquisition. To realise high precision and long range, we implement orthogonal optical readouts using cylindrical lenses. We demonstrate the performance of this new optical autofocus system with automated multiwell plate imaging and single molecule localisation microscopy and illustrate the benefit of using a superluminescent diode as the autofocus light source.</jats:p>
  • Journal article
    Thipparapu NK, Alam S, Wang Y, Pidishety S, Richardson DJ, Sahu JKet al., 2022,

    Widely Tunable Actively Mode-Locked Bi-Doped Fiber Laser Operating in the O-Band

    , IEEE PHOTONICS TECHNOLOGY LETTERS, Vol: 34, Pages: 711-714, ISSN: 1041-1135
  • Journal article
    Chung CH, Li J, Steuer CE, Bhateja P, Johnson M, Masannat J, Poole MI, Song F, Hernandez-Prera JC, Molina H, Wenig BM, Kumar S, Kuperwasser C, Stephens PJ, Farinhas JM, Shin DM, Kish JA, Muzaffar J, Kirtane K, Rocco JW, Schell MJ, Saba NF, Bonomi Met al., 2022,

    Phase II Multi-institutional Clinical Trial Result of Concurrent Cetuximab and Nivolumab in Recurrent and/or Metastatic Head and Neck Squamous Cell Carcinoma.

    , Clin Cancer Res, Vol: 28, Pages: 2329-2338

    PURPOSE: A phase II multi-institutional clinical trial was conducted to determine overall survival (OS) in patients with recurrent and/or metastatic (R/M) head and neck squamous cell carcinoma (HNSCC) treated with a combination of cetuximab and nivolumab. PATIENTS AND METHODS: Patients with R/M HNSCC were treated with cetuximab 500 mg/m2 i.v. on day 14 as a lead-in followed by cetuximab 500 mg/m2 i.v. and nivolumab 240 mg i.v. on day 1 and day 15 of each 28-day cycle. Expression of p16 and programmed cell death-ligand 1 (PD-L1) in archived tumors were determined. Tumor-tissue-modified human papillomavirus (TTMV) DNA was quantified in plasma. RESULTS: Ninety-five patients were enrolled, and 88 patients were evaluable for OS with a median follow-up of 15.9 months. Median OS in the 45 patients who had prior therapy for R/M HNSCC (cohort A) was 11.4 months, with a 1 year OS 50% [90% confidence interval (CI), 0.43-0.57]. Median OS in the 43 patients who had no prior therapy (cohort B) was 20.2 months, with a 1-year OS 66% (90% CI, 0.59-0.71). In the combined cohorts, the p16-negative immunostaining was associated with higher response rate (RR; P = 0.02) but did not impact survival while higher PD-L1 combined positive score was associated with higher RR (P = 0.03) and longer OS (log-rank P = 0.04). In the p16-positive patients, lower median (1,230 copies/mL) TTMV DNA counts were associated with higher RR (P = 0.01) and longer OS compared with higher median (log-rank P = 0.05). CONCLUSIONS: The combination of cetuximab and nivolumab is effective in patients with both previously treated and untreated R/M HNSCC and warrants further evaluation.
  • Journal article
    Van de Pette M, Dimond A, Galvao AM, Millership SJ, To W, Prodani C, McNamara G, Bruno L, Sardini A, Webster Z, McGinty J, French PMW, Uren AG, Castillo-Fernandez J, Watkinson W, Ferguson-Smith AC, Merkenschlager M, John RM, Kelsey G, Fisher Aet al., 2022,

    Epigenetic changes induced by in utero dietary challenge result in phenotypic variability in successive generations of mice

    , Nature Communications, Vol: 13, ISSN: 2041-1723

    Transmission of epigenetic information between generations occurs in nematodes, flies and plants, mediated by specialised small RNA pathways, modified histones and DNA methylation. Similar processes in mammals can also affect phenotype through intergenerational or trans-generational mechanisms. Here we generate a luciferase knock-in reporter mouse for the imprinted Dlk1 locus to visualise and track epigenetic fidelity across generations. Exposure to high-fat diet in pregnancy provokes sustained re-expression of the normally silent maternal Dlk1 in offspring (loss of imprinting) and increased DNA methylation at the somatic differentially methylated region (sDMR). In the next generation heterogeneous Dlk1 mis-expression is seen exclusively among animals born to F1-exposed females. Oocytes from these females show altered gene and microRNA expression without changes in DNA methylation, and correct imprinting is restored in subsequent generations. Our results illustrate how diet impacts the foetal epigenome, disturbing canonical and non-canonical imprinting mechanisms to modulate the properties of successive generations of offspring.
  • Conference paper
    Wysoczanski R, Baker JR, Fenwick P, Alexandrov Y, Dunsby C, French P, Barnes PJ, Donnelly LEet al., 2022,

    Defective Phagocytosis in COPD Macrophages Is Improved by Mitochondrial Antioxidants Without Alteration in Mitochondrial Function

    , International Conference of the American-Thoracic-Society, Publisher: AMER THORACIC SOC, ISSN: 1073-449X
  • Journal article
    Ahmad H, Hidayah Abdul Kahar N, Yusoff N, Zharif Samion M, Aisyah Reduan S, Faizal Ismail M, Bayang L, Wang Y, Wang S, Sahu JKet al., 2022,

    Passively Q-switched 1.3 μm bismuth doped-fiber laser based on transition metal dichalcogenides saturable absorbers

    , Optical Fiber Technology, Vol: 69, ISSN: 1068-5200

    In this work, Q-switched fiber laser has been demonstrated in a bismuth-doped fiber laser (BDFL) system using tungsten ditelluride (WTe2) and tungsten disulfide (WS2) as saturable absorbers (SAs). The solution casting method was used to prepare both WTe2 and WS2 thin films SAs. At the threshold pump power, the generation of Q-switched pulse using WTe2 SA resulted in a pulse width of 10.4μ s and a repetition rate of 21.20 kHz. When the pump power was increased to maximum, the pulse width reduced to 8.0μ s, while the repetition rates increased to 22.46 kHz. Similarly, a Q-switched pulse was generated using WS2 SA, with an initial repetition rate of 18.86 kHz and a pulse width of 14.4μ s. The repetition rate of the pulses then increased to 19.53 kHz and pulse width reduced to 11.2 μs with the increasing pump power. The maximum pulse energy obtained for WTe2 and WS2 SAs was 13.93 nJ and 11.36 nJ, respectively, with a maximum average output power of 0.313 mW (WTe2) and 0.222 mW (WS2). This work uses the transition metal dichalcogenides (TMDs) materials to generate Q-switched pulses in BDFL operating at 1.3 µm region.
  • Journal article
    Tawy G, Minassian A, Damzen MJ, 2022,

    Volume Bragg Grating Locked Alexandrite Laser

    , OPTICS, Vol: 3, Pages: 53-59
  • Journal article
    Hong W, Dunsby C, 2022,

    Automatic tube lens design from stock optics for microscope remote-refocusing systems

    , Optics Express, Vol: 30, Pages: 4274-4278, ISSN: 1094-4087

    The remote-refocusing approach of Botcherby et al. [Opt. Lett. 32, 2007 (2007) [CrossRef] ] has been applied widely to 2D and 3D fluorescence microscopes to enable rapid refocusing of the optical system without mechanically perturbing the sample. In order for this approach to operate correctly, it requires that the overall magnification of the first two microscope systems matches the ratio of the refractive indices in sample and intermedia image spaces. However, commercially available tube lenses are not always suitable to produce the desired overall magnification. Therefore, a practical approach to produce tube lenses with low expense and diffraction-limited performance is required. Tube lenses can be formed using a pair of stock achromatic doublets, however, selecting appropriate pairs of achromatic doublets from stock optics is a time-consuming process, as many combinations can be considered. In this paper, we present two software packages (Catalogue Generator and Doublet Selector) developed in MATLAB that use the application programming interface (ZOS-API) to the Zemax OpticStudio optical design software to realise an automatic search of stock achromatic doublets to produce microscope tube lenses with a specified focal length, entrance pupil diameter and maximum design field angle. An algorithm to optimise principal plane positions in versions of OpticStudio before 20.2 was also introduced to enable the use of older software versions. To evaluate the performance of Catalogue Generator and Doublet Selector, we used them to generate ten tube lens designs. All of the software-produced tube lenses have a better optical performance than those using manually selected pairs of stock doublets lenses.
  • Conference paper
    Murray RT, Anderson J, Wei J, Zawilski KT, Schunemann PG, Guha Set al., 2022,

    Wavelength tunable mid-infrared generation in non-critically cut CdSiP<inf>2</inf> crystals by cascaded optical parametric generation with a nanosecond 1.064 µm Nd:YAG laser

    We demonstrate a method to generate wavelength tunable mid-infrared radiation from 3.7-4.3 µm using a nanosecond 1.064 µm Nd:YAG pump at 10 Hz, employing cascaded optical parametric generation in non-critically cut CdSiP2 crystals.
  • Conference paper
    Hong Y, Taengnoi N, Bottrill KRH, Wang Y, Sahu JK, Petropoulos P, Richardson DJet al., 2022,

    Demonstration of up to 480-km BDFA-based WDM Direct-detection Transmission in the O-band

    We report on experiments of 3×50-Gb/s O-band WDM direct-detection transmission using a BDFA-based optical recirculating loop. Record-long transmission distances up to 480 km are achieved at the SD-FEC limit in experiments with two different channel spacings.
  • Journal article
    Hong Y, Deligiannidis S, Taengnoi N, Bottrill KRH, Thipparapu NK, Wang Y, Sahu JK, Richardson DJ, Mesaritakis C, Bogris A, Petropoulos Pet al., 2022,

    ML-Assisted Equalization for 50-Gb/s/λ O-Band CWDM Transmission Over 100-km SMF

    , IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS, Vol: 28, ISSN: 1077-260X
  • Conference paper
    Zhai Z, Halder A, Wang Y, Nunez-Velazquez M, Sahu JKet al., 2022,

    Temperature Dependent Characteristics of L-band EDFA Using Phosphorus- and High Aluminum-Co-doped Silica Fibers

    We report a hybrid L-band amplifier employing phosphosilicate and high-aluminosilicate EDFs with 20.2±3.7dB gain and 4.2dB average NF from 1575-1615nm. The temperature-dependent-gain coefficient remains almost constant from 1585-1615nm over the temperature range -60 to +80°C.
  • Conference paper
    Zhai Z, Halder A, Wang Y, Núñez-Velázquez M, Sahu JKet al., 2022,

    Temperature Dependent Characteristics of L-band EDFA Using Phosphorus- and High Aluminum- Co-doped Silica Fibers

    We report a hybrid L-band amplifier employing phosphosilicate and high-aluminosilicate EDFs with 20.2±3.7dB gain and 4.2dB average NF from 1575-1615nm. The temperature-dependent-gain coefficient remains almost constant from 1585-1615nm over the temperature range -60 to +80°C.
  • Conference paper
    Murray RT, Anderson J, Wei J, Zawilski KT, Schunemann PG, Guha Set al., 2022,

    Wavelength tunable mid-infrared generation in non-critically cut CdSiP<inf>2</inf> crystals by cascaded optical parametric generation with a nanosecond 1.064 μm Nd:YAG laser

    We demonstrate a method to generate wavelength tunable mid-infrared radiation from 3.7-4.3 μm using a nanosecond 1.064 μm Nd:YAG pump at 10 Hz, employing cascaded optical parametric generation in non-critically cut CdSiP2 crystals.
  • Conference paper
    Hong Y, Taengnoi N, Bottrill KRH, Wang Y, Sahu JK, Petropoulos P, Richardson DJet al., 2022,

    550-km Amplified Direct-Detection Transmission at 1.3μm

    We report on transmission experiments in the O-band using a bismuth-doped fiber amplifier-based optical recirculating loop. Distances up to a record length of 550 km are demonstrated in a 50-Gb/s direct-detection system at the soft-decision forward error correction limit.
  • Conference paper
    Battle RA, Chandran AM, Runcorn TH, Mussot A, Kudlinski A, Murray RT, Taylor JRet al., 2022,

    Optical parametric amplification seeded by four-wave mixing in photonic crystal fibers

    , Conference on Nonlinear Frequency Generation and Conversion - Materials and Devices XXI at SPIE LASE Conference, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X
  • Conference paper
    Fox MFJ, Bland S, Mangles SPD, McGinty Jet al., 2022,

    Expectations of how student views on experimental physics develop during an undergraduate degree

    , Physics Education Research Conference (PERC), Publisher: AMER ASSOC PHYSICS TEACHERS, Pages: 182-187, ISSN: 2377-2379
  • Conference paper
    Codescu M-A, Weiß M, Brehm M, Kornilov O, Sebastiani D, Nibbering ETJet al., 2022,

    Ultrafast Proton Transfer Pathways Mediated by Imidazole

    , International Conference on Ultrafast Phenomena, Publisher: Optica Publishing Group

    <jats:p>We explore with ultrafast infrared spectroscopy and molecular dynamics simulations how imidazole, an amphoteric molecule that can act both as acid and as base, provides alternate proton transfer pathways in the tautomerization reaction of 7-hydroxyquinoline.</jats:p>
  • Journal article
    Ramuz M, Diakonov I, Dunsby C, Gorelik Jet al., 2022,

    MultiFRET: A Detailed Protocol for High-Throughput Multiplexed Ratiometric FRET.

    , Methods Mol Biol, Vol: 2483, Pages: 33-59

    The newly generated software plugin MultiFRET allows for real-time measurements of multiplexed fluorescent biosensors in a near high-throughput fashion. Here we describe a detailed protocol for setup and use of this software for any purpose requiring instant feedback during fluorescence measurement experiments. We further describe its non-primary features including beam splitter misalignment correction, custom calculations through input of simple equations typed in a .txt format, customizable Excel output, and offline bulk analysis of image stacks. Finally, we supply a usage example of a cAMP measurement in cultured rat neonatal cardiomyocytes.
  • Journal article
    Ahmad H, Kamaruddin NH, Aidit SN, Samion MZ, K A Zaini M, Bayang L, Wang Y, Wang S, Sahu JK, Yasin Met al., 2021,

    Multi-wavelength Bismuth-doped fiber laser in 1.3 µm based on a compact two-mode fiber filter

    , Optics and Laser Technology, Vol: 144, ISSN: 0030-3992

    In this work, a multi-wavelength Bismuth-doped fiber laser (MWLBDFL) operating in the 1.3 µm wavelength region is presented and experimentally demonstrated. The MWLBDFL leveraged on a 60 m Bismuth-doped fiber as an active gain medium, a compact two-mode fiber filter (TMFF) as a comb filter and a 2 km single-mode fiber section to induce four-wave mixing in the system. By optimising the polarization controller, the MWLBDFL generated 18 stable lasing output channels within 10 dB from the highest lasing line and a reasonably flat spectrum over a range of 11 nm. The stability of the MWLBDFL tested for a 150-minute duration showed a peak power fluctuation of less than 1 dB with a negligible wavelength drift. The extinction ratio of the TMFF was approximately 8.6 dB while the highest and lowest optical-signal-to-noise ratios (OSNRs) of the MWLBDFL were ~ 55 dB and ~ 50 dB, respectively. To the best of the author's knowledge, the proposed MWLBDFL demonstrates the highest number of output channels compared to other MWLs operating in the same wavelength region.
  • Journal article
    Kalita R, Flanagan W, Lightley J, Kumar S, Alexandrov Y, Garcia E, Hintze M, Barkoulas M, Dunsby C, French PMWet al., 2021,

    Single-shot phase contrast microscopy using polarisation-resolved differential phase contrast

    , JOURNAL OF BIOPHOTONICS, Vol: 14, ISSN: 1864-063X

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